The National Audit Office (NAO) is to re-examine the NHS's £6.2bn nationwide computer overhaul just two months after giving the 10-year project - the largest non-military IT programme in the world - a clean bill of health.

The government spending watchdog refused yesterday to be drawn on why it was turning its attention back to the NHS's National Programme for IT (NPfIT) so soon after its largely uncritical 63-page report in June. That report praised the "substantial progress" it had made.

The report said: "Deployments of operational systems have begun and Connecting for Health [the NHS's IT procurement arm] has taken on, and in some cases already delivered, several additional tasks which were not within the original brief ... The notable progress and tight control of the central aspect of the programme are to be commended."

The decision to re-examine the NPfIT - revealed in today's Computer Weekly magazine - comes after embarrassing revelations about how the wording and emphasis in the June report had been watered down from early drafts.

Since June, a catalogue of problems linked to the NPfIT have emerged. The Guardian revealed last month that two of the NHS's lead contractors had serious concerns about next-generation software, called Lorenzo, earmarked for 60% of England's GP practices and hospitals, which was being developed by the financially stretched firm iSoft. The lead contractors Accenture and CSC had concluded in February that Lorenzo had "no believable plan for releases".

The Guardian also revealed that the Financial Services Authority was investigating past accounting irregularities at iSoft, which had suspended its co-founder Steven Graham. ISoft then posted a £382m loss for the year to April and admitted its auditor, Deloitte, had been unable to sign off the accounts because of changes to accounting policies. The group's lenders extended banking facilities for 15 months, but only at onerous rates of interest.

Elsewhere, Accenture, which is responsible for deploying NPfIT software in the north-east and eastern England, has all but halted work on elements of NPfIT and is believed to be seeking to retreat from much of its NHS work. In March, it made a $450m (£236m) provision against future losses from NPfIT contracts, partly blaming delays on iSoft.

BT, which is responsible for deploying NPfIT software in London, is believed to have spent more than £200m on the project, but has been paid just £1.3m by Connecting for Health for two years' work.

Meanwhile, about 10 NHS trusts are believed to have become so disillusioned with the NPfIT that they have opted out, forgoing millions of pounds of state funding in favour of selecting their own IT systems paid for from already overstretched budgets. Polls have also suggested waning support for NPfIT among NHS staff.

A second NAO report into the NPfIT is again likely to be limited, as a technical review is beyond its expertise.

There have already been a number of setbacks to patient administration systems - the only NPfIT system to have been deployed in hospitals so far. A failure at a data centre caused systems at 80 hospitals to collapse for about four days last month, which is the NHS's biggest IT failure ever. A data recovery system failed to provide backup.

The Commons health select committee is expected to examine the National Programme this autumn and could call on the government to order a full review. Meanwhile, there have been cross-party calls from MPs for the trade and industry secretary, Alistair Darling, to appoint inspectors under the Companies Act to investigate accounting irregularities at iSoft.